I dont think there is a problem in people starting aikido because of a story like this. However there is a problem with people presenting a story like this as fact. This gives the the false idea that you will eventually be able to dodge bullets. This is just as bad as telling someone they can put up a ki shield to prevent all damage done to them by strikes, or that they can knock someone out with astrial spirts.

There are a lot of myths around most important cultural figures. They should be presented as such. Without knowing all the facts, and with only a single stroy to use as evidence (which you can't technically do), we can only call this a myth. It is still a great story though.

Of course there are plusable explainations as to how he could dodge bullets. I myself have dodged paintballs. However, every explaination simply points to the fact that the shooters were aiming at a spot, and not aiming at O'Sensei. But perhaps it was his training that allowed him to see that was the case and to not give up like he did with the sniper.